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Elusive Origins of the Extra Genes in Aspergillus oryzae

The genome sequence of Aspergillus oryzae revealed unexpectedly that this species has approximately 20% more genes than its congeneric species A. nidulans and A. fumigatus. Where did these extra genes come from? Here, we evaluate several possible causes of the elevated gene number. Many gene familie...

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Autores principales: Khaldi, Nora, Wolfe, Kenneth H.
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2515630/
https://www.ncbi.nlm.nih.gov/pubmed/18725939
http://dx.doi.org/10.1371/journal.pone.0003036
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author Khaldi, Nora
Wolfe, Kenneth H.
author_facet Khaldi, Nora
Wolfe, Kenneth H.
author_sort Khaldi, Nora
collection PubMed
description The genome sequence of Aspergillus oryzae revealed unexpectedly that this species has approximately 20% more genes than its congeneric species A. nidulans and A. fumigatus. Where did these extra genes come from? Here, we evaluate several possible causes of the elevated gene number. Many gene families are expanded in A. oryzae relative to A. nidulans and A. fumigatus, but we find no evidence of ancient whole-genome duplication or other segmental duplications, either in A. oryzae or in the common ancestor of the genus Aspergillus. We show that the presence of divergent pairs of paralogs is a feature peculiar to A. oryzae and is not shared with A. nidulans or A. fumigatus. In phylogenetic trees that include paralog pairs from A. oryzae, we frequently find that one of the genes in a pair from A. oryzae has the expected orthologous relationship with A. nidulans, A. fumigatus and other species in the subphylum Eurotiomycetes, whereas the other A. oryzae gene falls outside this clade but still within the Ascomycota. We identified 456 such gene pairs in A. oryzae. Further phylogenetic analysis did not however indicate a single consistent evolutionary origin for the divergent members of these pairs. Approximately one-third of them showed phylogenies that are suggestive of horizontal gene transfer (HGT) from Sordariomycete species, and these genes are closer together in the A. oryzae genome than expected by chance, but no unique Sordariomycete donor species was identifiable. The postulated HGTs from Sordariomycetes still leave the majority of extra A. oryzae genes unaccounted for. One possible explanation for our observations is that A. oryzae might have been the recipient of many separate HGT events from diverse donors.
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spelling pubmed-25156302008-08-22 Elusive Origins of the Extra Genes in Aspergillus oryzae Khaldi, Nora Wolfe, Kenneth H. PLoS One Research Article The genome sequence of Aspergillus oryzae revealed unexpectedly that this species has approximately 20% more genes than its congeneric species A. nidulans and A. fumigatus. Where did these extra genes come from? Here, we evaluate several possible causes of the elevated gene number. Many gene families are expanded in A. oryzae relative to A. nidulans and A. fumigatus, but we find no evidence of ancient whole-genome duplication or other segmental duplications, either in A. oryzae or in the common ancestor of the genus Aspergillus. We show that the presence of divergent pairs of paralogs is a feature peculiar to A. oryzae and is not shared with A. nidulans or A. fumigatus. In phylogenetic trees that include paralog pairs from A. oryzae, we frequently find that one of the genes in a pair from A. oryzae has the expected orthologous relationship with A. nidulans, A. fumigatus and other species in the subphylum Eurotiomycetes, whereas the other A. oryzae gene falls outside this clade but still within the Ascomycota. We identified 456 such gene pairs in A. oryzae. Further phylogenetic analysis did not however indicate a single consistent evolutionary origin for the divergent members of these pairs. Approximately one-third of them showed phylogenies that are suggestive of horizontal gene transfer (HGT) from Sordariomycete species, and these genes are closer together in the A. oryzae genome than expected by chance, but no unique Sordariomycete donor species was identifiable. The postulated HGTs from Sordariomycetes still leave the majority of extra A. oryzae genes unaccounted for. One possible explanation for our observations is that A. oryzae might have been the recipient of many separate HGT events from diverse donors. Public Library of Science 2008-08-22 /pmc/articles/PMC2515630/ /pubmed/18725939 http://dx.doi.org/10.1371/journal.pone.0003036 Text en Khaldi et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Khaldi, Nora
Wolfe, Kenneth H.
Elusive Origins of the Extra Genes in Aspergillus oryzae
title Elusive Origins of the Extra Genes in Aspergillus oryzae
title_full Elusive Origins of the Extra Genes in Aspergillus oryzae
title_fullStr Elusive Origins of the Extra Genes in Aspergillus oryzae
title_full_unstemmed Elusive Origins of the Extra Genes in Aspergillus oryzae
title_short Elusive Origins of the Extra Genes in Aspergillus oryzae
title_sort elusive origins of the extra genes in aspergillus oryzae
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2515630/
https://www.ncbi.nlm.nih.gov/pubmed/18725939
http://dx.doi.org/10.1371/journal.pone.0003036
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